Nathan Sheffield

Hey @johanneskoester -- it would be possible to *not* use the `SnakeProject` class if you instead subscribed to the original PEP names (like `subsample` instead of `unit`). All the rest...

For your first point: we are also planning to adopt the snakemake (or similar) validation for PEPs as well. So, sounds good. we should address that soon. For your second...

@johanneskoester, @vreuter -- where do we stand on this? I agree we can easily make this parameterizable. I think we should use `subsample_name` and not `unit` as the default. but...

indexes are parameterize, not names. > With the parameter to Project I did not mean to make the column name parameterizable, but rather wanted to give the user the possibility...

Has there been any update on effort to standardize the `workflow_params`?

this opens the possibility of asset classes... the txfasta asset is of class 'fasta' without being identical. we can decouple the recipe from the seek keys. the asset class would...

that's kind of funny. I bet it comes from where we are teeing the output. probably destroying the pipelinemanager would work because that would break the Tee. But any way...

Yes, you can. Instructions are here: http://refgenie.databio.org/en/latest/build/ just do get a fasta file with the mtdna you want and do: ``` refgenie build dm_mtDNA/fasta --files fasta=dm_mtDNA.fa.gz ```

These are great suggestions. We will definitely work on adding the date and versions to the splash page. As for the salmon indexes -- @k3yavi, do you need us to...

@tamuanand if you need to build the ensembl-based indexes, you can do so with `refgenie build`, since we're only hosting the NCBI one right now.